Opened 2 years ago

Closed 2 years ago

#9709 closed defect (can't reproduce)

Dead region in sequence-associated regions

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/marcello/Downloads/ChimeraX/AlphaFold/prediction_1/best_model.pdb
> format pdb

Chain information for best_model.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open 6i6h

6i6h title:  
Crystal structure of the KDEL receptor in the peptide bound state [more
info...]  
  
Chain information for 6i6h #2  
---  
Chain | Description | UniProt  
A | ER lumen protein-retaining receptor 2 | ERD22_CHICK 1-207  
B | AEKDEL peptide |  
  
Non-standard residues in 6i6h #2  
---  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-Oleoyl-R-glycerol)  
  

> open
> "/Users/marcello/Library/CloudStorage/Dropbox/GuLLab/Projects/GABARAP/Alphafold/CALR_AF-P27797-F1-model_v4
> .pdb"

CALR_AF-P27797-F1-model_v4 .pdb title:  
Alphafold monomer V2.0 prediction for calreticulin (P27797) [more info...]  
  
Chain information for CALR_AF-P27797-F1-model_v4 .pdb #3  
---  
Chain | Description | UniProt  
A | calreticulin | CALR_HUMAN 1-417  
  

> select add #3

3399 atoms, 3486 bonds, 417 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,47.042,0,1,0,73.106,0,0,1,26.193

> ui mousemode right "rotate selected models"

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> view matrix models #3,1,0,0,-104.26,0,1,0,-70.108,0,0,1,-49.633

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.6127,-0.31246,-0.72592,-94.833,-0.45231,0.61459,-0.6463,-60.653,0.64808,0.72433,0.23523,-50.119

> view matrix models
> #3,0.77509,-0.30663,-0.55246,-98.68,-0.24853,0.65592,-0.71274,-63.253,0.58091,0.68974,0.4322,-50.635

> view matrix models
> #3,0.98533,0.0078543,-0.17049,-102.77,-0.15594,-0.36461,-0.91801,-69.993,-0.069372,0.93113,-0.35803,-32.822

> view matrix models
> #3,-0.54718,0.06695,0.83433,-84.358,-0.32219,0.90314,-0.28377,-63.458,-0.77252,-0.42409,-0.47262,-29.35

> view matrix models
> #3,-0.72317,0.59142,-0.35673,-69.637,-0.66142,-0.44432,0.60423,-72.976,0.19885,0.67291,0.71249,-46.463

> view matrix models
> #3,-0.5811,-0.39331,-0.71248,-75.892,-0.75583,-0.063763,0.65166,-69.276,-0.30173,0.91719,-0.26022,-29.796

> view matrix models
> #3,-0.53363,-0.48163,-0.69518,-77.37,-0.73084,-0.15101,0.66563,-70.354,-0.42556,0.86327,-0.27141,-28.04

> view matrix models
> #3,-0.57247,-0.70814,-0.4133,-80.204,-0.74963,0.24784,0.6137,-67.072,-0.33215,0.66115,-0.67273,-28.059

> view matrix models
> #3,-0.594,-0.54628,-0.59055,-77.542,-0.76425,0.15399,0.62626,-67.535,-0.25118,0.82332,-0.50897,-29.482

> view matrix models
> #3,-0.40493,-0.8047,-0.43415,-83.434,-0.63907,-0.090503,0.7638,-72.156,-0.65393,0.58674,-0.47761,-24.65

> view matrix models
> #3,-0.59441,-0.5452,-0.59113,-77.524,-0.76446,0.15498,0.62577,-67.522,-0.24955,0.82386,-0.5089,-29.505

> view matrix models
> #3,-0.9366,-0.33133,-0.11406,-73.885,-0.21426,0.28394,0.9346,-77.875,-0.27727,0.89978,-0.33693,-29.769

> view matrix models
> #3,-0.8971,-0.43237,-0.090915,-75.357,-0.19154,0.19516,0.96189,-79.021,-0.39815,0.88032,-0.25789,-28.473

> view matrix models
> #3,-0.87551,-0.48171,-0.037991,-76.407,-0.12239,0.14501,0.98183,-80.622,-0.46744,0.86425,-0.18592,-27.951

> view matrix models
> #3,-0.53883,-0.65024,0.53558,-87.075,0.40124,0.36092,0.84187,-86.804,-0.74072,0.66852,0.066432,-26.533

> view matrix models
> #3,-0.61773,-0.78067,0.094736,-83.523,-0.09246,0.19173,0.97708,-80.774,-0.78094,0.59481,-0.19062,-24.541

> view matrix models
> #3,-0.42894,-0.84212,0.32687,-88.657,0.23317,0.24637,0.94071,-85.496,-0.87272,0.47973,0.090676,-25.775

> view matrix models
> #3,-0.35901,-0.85138,0.38245,-90.256,0.32412,0.27054,0.90651,-86.587,-0.87525,0.44941,0.17882,-26.554

> view matrix models
> #3,-0.56683,-0.70905,0.41946,-86.181,-0.1267,0.57813,0.80605,-76.479,-0.81404,0.40375,-0.41753,-23.646

> view matrix models
> #3,-0.57061,-0.66521,0.48157,-86.271,-0.047601,0.61221,0.78926,-77.434,-0.81984,0.42744,-0.38099,-23.654

> view matrix models
> #3,-0.57406,-0.63006,0.52294,-86.276,0.012428,0.63189,0.77496,-78.188,-0.81872,0.45138,-0.35491,-23.7

> view matrix models
> #3,-0.98545,-0.14774,-0.083987,-72.097,-0.079158,-0.038273,0.99613,-82.63,-0.15038,0.98829,0.026021,-33.832

> ui mousemode right "move picked models"

> view matrix models
> #3,-0.98545,-0.14774,-0.083987,-70.473,-0.079158,-0.038273,0.99613,-89.046,-0.15038,0.98829,0.026021,-25.919

> ui mousemode right "rotate selected models"

> ui mousemode right translate

[Repeated 1 time(s)]

> select subtract #3

Nothing selected  

> select add #2

2115 atoms, 2014 bonds, 361 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,11.518,0,1,0,18.923,0,0,1,-37.946

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.52651,-0.57522,-0.62603,149.53,0.84165,-0.45666,-0.28826,63.552,-0.12007,-0.67867,0.72456,15.968

> hide sel atoms

> view matrix models
> #2,-0.5148,-0.63771,-0.57298,147.03,0.84222,-0.50106,-0.19903,58.001,-0.16017,-0.58503,0.79504,8.7149

> view matrix models
> #2,-0.69039,-0.0087002,-0.72338,144.03,0.71649,0.13004,-0.68537,79.576,0.10004,-0.99147,-0.083548,82.176

> view matrix models
> #2,-0.55564,-0.44698,-0.70105,152.17,0.82989,-0.34931,-0.43504,71.916,-0.050429,-0.82352,0.56504,30.891

> view matrix models
> #2,-0.54556,-0.48856,-0.68094,151.62,0.83502,-0.38613,-0.39197,69.581,-0.071431,-0.78244,0.61861,26.048

> view matrix models
> #2,-0.53122,-0.5525,-0.6423,150.21,0.8405,-0.43907,-0.31746,65.3,-0.10662,-0.70849,0.69762,18.608

> view matrix models
> #2,-0.56211,-0.42138,-0.71167,152.37,0.82618,-0.32578,-0.45967,73.197,-0.038155,-0.84635,0.53126,33.876

> ui mousemode right translate

> select subtract #2

Nothing selected  
Alignment identifier is 1/A  
Alignment identifier is 2/A  
Alignment identifier is 2/B  
Alignment identifier is 3/A  

> color #2 #c2e5efff

> color #1 #d6dba8ff

> color #3 #e5d0dbff

> color #3 #e5c4dbff

> select #3/A:414

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/A:414-417

35 atoms, 34 bonds, 4 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> style sel ball

Changed 35 atom styles  

> style sel ball

Changed 35 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 35 atom styles  

> style sel sphere

Changed 35 atom styles  

> style sel sphere

Changed 35 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 35 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> show sel surfaces

[Repeated 1 time(s)]

> color #3.1 #b73b87ff

> color #3.1 #76069aff

> select #1/A:414

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #1/A:414-417

34 atoms, 33 bonds, 4 residues, 1 model selected  

> show sel atoms

> show sel surfaces

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> color #1.1 #76069aff

> select #1/A:413

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:316-413

816 atoms, 824 bonds, 98 residues, 1 model selected  

> select #1/A:413-414

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #1/A:133-414

2328 atoms, 2388 bonds, 282 residues, 1 model selected  

> select #1/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1-413

3364 atoms, 3451 bonds, 413 residues, 1 model selected  

> show sel cartoons

[Repeated 2 time(s)]

> sequence disassociate #1/A

Disassociated best_model.pdb chain A from chain A  

> select add #1

6182 atoms, 6329 bonds, 776 residues, 2 models selected  

> select subtract #1

1 model selected  

> select add #1

6182 atoms, 6329 bonds, 776 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> rainbow

> undo

> interfaces ~solvent

1 buried areas: #2/A #2/B 552  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 0 maps.  

[Repeated 1 time(s)]

> select add #1

6182 atoms, 6329 bonds, 776 residues, 1 model selected  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 3 atomic
models, 0 maps.  

[Repeated 1 time(s)]

> set bgColor white

> color #1 #b73b87ff

> color #1.1 #6dc66dff

> color #1.1 green

> color #2 #2294b2ff

> color #3 #b73b87ff

> color #3.1 green

> select subtract #1

1 model selected  

> save "/Users/marcello/Dropbox
> (Personal)/GuLLab/Projects/GABARAP/Alphafold/CALR-3xHA-TurboID all
> three.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/tool.py", line 781, in take_snapshot  
'region browser': self.region_browser.state(),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in state  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <dictcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <listcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
ValueError: <chimerax.seq_view.region_browser.Region object at 0x17b90a190> is
not in list  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x112520250> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at
0x16398bc40>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/tool.py", line 781, in take_snapshot  
'region browser': self.region_browser.state(),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in state  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <dictcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <listcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
ValueError: <chimerax.seq_view.region_browser.Region object at 0x17b90a190> is
not in list  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x112520250> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at
0x16398bc40>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  

> save "/Users/marcello/Dropbox
> (Personal)/GuLLab/Projects/GABARAP/Alphafold/CALR and KDELR.cxs"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/tool.py", line 781, in take_snapshot  
'region browser': self.region_browser.state(),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in state  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <dictcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <listcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
ValueError: <chimerax.seq_view.region_browser.Region object at 0x17b90a190> is
not in list  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x112520250> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at
0x16398bc40>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/tool.py", line 781, in take_snapshot  
'region browser': self.region_browser.state(),  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in state  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <dictcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seq_view/region_browser.py", line 1121, in <listcomp>  
state['sequence_regions'] = { k: [ self.regions.index(r) for r in v ]  
ValueError: <chimerax.seq_view.region_browser.Region object at 0x17b90a190> is
not in list  
  
The above exception was the direct cause of the following exception:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 290, in process  
raise RuntimeError(msg) from e  
RuntimeError: Error while saving session data for 'tools' ->
<chimerax.core.tools.Tools object at 0x112520250> ->
<chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at 0x16398bc40>:
Error while saving session data for 'tools' -> <chimerax.core.tools.Tools
object at 0x112520250> -> <chimerax.seq_view.tool.SequenceViewer object at
0x16398bc40>  
  
ValueError: error processing: 'tools' -> -> : Error while saving session data
for 'tools' -> ->  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: MYD92T/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (c) (22F770820d)
      Kernel Version: Darwin 22.5.0
      Time since boot: 14 days, 21 hours, 14 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        ASUS VS207:
          Resolution: 1600 x 900
          UI Looks like: 1600 x 900 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Dead region in sequence-associated regions

comment:2 by Eric Pettersen, 2 years ago

Resolution: → can't reproduce
Status: accepted → closed

I don't even see where they opened an alignment!

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